Payroll Manager Eden Prairie, MN

Payroll Manager

We are looking for an experienced Payroll Manager to lead payroll operations for a non-profit organization in Eden Prairie, Minnesota. This long-term contract position is ideal for a payroll specialist who can drive accurate processing, maintain strong tax compliance, and support financial integrity across a complex multi-state environment. The role will also partner closely with HR, Accounting, benefits teams, and external vendors to strengthen processes, resolve issues, and ensure dependable payroll service for employees.

Responsibilities:

• Direct end-to-end payroll execution across recurring biweekly and semi-monthly cycles, ensuring employees are paid accurately and on schedule.
• Guide payroll tax administration by managing registrations, reconciliations, filings, and regulatory updates across federal, state, and local jurisdictions.
• Oversee quarter-end and year-end payroll activities, including preparation and review of W-2 and W-2C processing.
• Administer payroll system setup and maintenance, including organizational structures, pay groups, earnings, deductions, and general ledger mappings.
• Act as the main point of contact for payroll system support, coordinating troubleshooting, testing, enhancements, and issue resolution with external partners.
• Manage benefit deduction processing and reconciliation while working with Human Resources, Accounting, and vendors to address billing and funding needs.
• Ensure payroll results are properly reflected in accounting records and support monthly, quarterly, and annual financial reporting requirements.
• Investigate payroll variances or accounting discrepancies and collaborate with internal stakeholders to implement timely resolutions.
• Lead, coach, and develop payroll team members by setting priorities, reinforcing accountability, and encouraging cross-training and growth.
• Identify opportunities to improve payroll procedures, internal controls, efficiency, and scalability through strong cross-functional partnership.